Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,919,873 G→A D24N (GAT→AAT)  b1836 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,919,8730GA99.2% 440.0 / ‑5.1 125D24N (GAT→AAT) b1836hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (55/69);  total (55/70)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.47e-01

Only 100 of 129 total aligned reads displayed.

AGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTG  >  NC_000913/1919783‑1919962
                                                                                          |                                                                                         
aGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAAt                                                                                         >  1:248189/1‑93 (MQ=255)
aGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAAt                                                                                         <  1:177889/93‑1 (MQ=255)
 gCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATc                                                                                        >  2:255982/1‑93 (MQ=255)
  cTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCg                                                                                       >  1:1775051/1‑93 (MQ=255)
  cTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCg                                                                                       >  2:3277782/1‑93 (MQ=255)
    aaaTGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGaa                                                                                     >  2:1400148/1‑93 (MQ=255)
    aaaTGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGaa                                                                                     <  2:2131358/93‑1 (MQ=255)
       tGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGt                                                                                  <  1:2989263/93‑1 (MQ=255)
       tGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGt                                                                                  >  2:3917421/1‑93 (MQ=255)
        ggAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGtt                                                                                 >  2:4481972/1‑93 (MQ=255)
        ggAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGtt                                                                                 <  2:3988329/93‑1 (MQ=255)
         gagaGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATTGCGAGGTAATCGAACggga                                                                                >  1:2074817/1‑90 (MQ=255)
           gagCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAAc                                                                              >  1:1755239/1‑93 (MQ=255)
           gagCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAAc                                                                              <  2:2427099/93‑1 (MQ=255)
             gCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCa                                                                            >  2:86186/1‑93 (MQ=255)
             gCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCa                                                                            >  1:1539429/1‑93 (MQ=255)
              gaCGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCAt                                                                           <  2:3589198/92‑1 (MQ=255)
              cACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCAt                                                                           <  2:2831195/93‑1 (MQ=255)
                cGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTc                                                                         <  1:4684164/93‑1 (MQ=255)
                 gAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTcc                                                                        >  2:614561/1‑93 (MQ=255)
                  aaGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCt                                                                       >  2:3279191/1‑93 (MQ=255)
                  aaGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCt                                                                       <  2:1028884/93‑1 (MQ=255)
                  aaGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCt                                                                       >  1:2337670/1‑93 (MQ=255)
                   aGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCtt                                                                      <  1:616143/93‑1 (MQ=255)
                    gATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAGTCGCCAGGTAATCGAACGTTAACCATTCGTTg                                                                     >  1:1707711/1‑93 (MQ=255)
                      tGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTa                                                                   >  2:4316745/1‑93 (MQ=255)
                      tGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTa                                                                   <  1:3367894/93‑1 (MQ=255)
                        aaaaCCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTaaa                                                                 <  2:2011313/93‑1 (MQ=255)
                        aaaaCCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTaaa                                                                 <  2:1393948/93‑1 (MQ=255)
                          aaCCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATc                                                               <  1:2211409/93‑1 (MQ=255)
                          aaCCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATc                                                               <  1:4510262/93‑1 (MQ=255)
                          aaCCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATc                                                               <  1:987573/93‑1 (MQ=255)
                            ccAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTg                                                             <  2:2486013/93‑1 (MQ=255)
                            ccAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTg                                                             >  2:2795038/1‑93 (MQ=255)
                              aGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGAc                                                           <  1:3202744/93‑1 (MQ=255)
                              aGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGAc                                                           >  1:1970092/1‑93 (MQ=255)
                               gtgtGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGAcc                                                          >  2:3714685/1‑93 (MQ=255)
                                tgtgCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGAccc                                                         <  2:3179977/93‑1 (MQ=255)
                                   gcgcATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGa                                                      <  2:4219928/93‑1 (MQ=255)
                                    cgcATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGAt                                                     <  1:4223261/93‑1 (MQ=255)
                                    cgcATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGAt                                                     <  1:3403878/93‑1 (MQ=255)
                                     gcATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGAtt                                                    >  1:4256911/1‑93 (MQ=255)
                                       aTAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTta                                                  <  1:3196289/93‑1 (MQ=255)
                                       aTAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTta                                                  <  2:316757/93‑1 (MQ=255)
                                        tAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtat                                                 <  2:3644372/93‑1 (MQ=255)
                                          ggCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgt                                               <  1:2590539/93‑1 (MQ=255)
                                          ggCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgt                                               >  1:2941276/1‑93 (MQ=255)
                                           gcgcTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgta                                              >  1:3569414/1‑93 (MQ=255)
                                            cgcTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgtat                                             <  2:3138718/93‑1 (MQ=255)
                                            cgcTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgtat                                             <  1:3437290/93‑1 (MQ=255)
                                             gcTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTtatgtatg                                            >  2:1865580/1‑93 (MQ=255)
                                              cTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGc                                           <  2:1858304/93‑1 (MQ=255)
                                               ttttGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCa                                          >  1:567614/1‑93 (MQ=255)
                                               ttttGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCa                                          >  1:731239/1‑93 (MQ=255)
                                               ttttGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCa                                          <  2:1608171/93‑1 (MQ=255)
                                                tttGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCaa                                         <  1:769463/93‑1 (MQ=255)
                                                 ttGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAAc                                        <  1:4448567/93‑1 (MQ=255)
                                                  tGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACt                                       <  2:1061624/93‑1 (MQ=255)
                                                   gAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTg                                      <  1:4258450/93‑1 (MQ=255)
                                                   gAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTg                                      >  1:2511084/1‑93 (MQ=255)
                                                     aaTCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGa                                    <  1:1188827/93‑1 (MQ=255)
                                                     aaTCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGa                                    <  1:1778938/93‑1 (MQ=255)
                                                      aTCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGAt                                   <  2:3879213/93‑1 (MQ=255)
                                                        cgacgaCGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGc                                 >  2:809635/1‑93 (MQ=255)
                                                         gacgacGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGcc                                >  2:3265881/1‑93 (MQ=255)
                                                         gacgacGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGcc                                <  1:4339050/93‑1 (MQ=255)
                                                         gacgacGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGcc                                >  1:2860103/1‑93 (MQ=255)
                                                         gacgacGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATATGACCCCGATTTATGTATGCAACTGGATGcc                                >  2:4396518/1‑93 (MQ=255)
                                                         cacgacgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATCCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGcc                                <  2:3641770/92‑1 (MQ=255)
                                                           cgacgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTg                              <  1:4427708/93‑1 (MQ=255)
                                                           cgacgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTg                              <  1:4126657/93‑1 (MQ=255)
                                                            gacgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTgg                             <  1:4425033/93‑1 (MQ=255)
                                                            gacgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTgg                             <  2:532219/93‑1 (MQ=255)
                                                             acgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTggg                            >  1:5754/1‑93 (MQ=255)
                                                              cgGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGa                           <  1:219642/93‑1 (MQ=255)
                                                               ggCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGAt                          <  1:1115350/93‑1 (MQ=255)
                                                                gCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATg                         >  1:2325473/1‑93 (MQ=255)
                                                                  gAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCt                       <  2:4417884/93‑1 (MQ=255)
                                                                  gAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCt                       <  2:2285533/93‑1 (MQ=255)
                                                                  gAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCt                       <  2:1346924/93‑1 (MQ=255)
                                                                   aaTTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTg                      >  1:1197233/1‑93 (MQ=255)
                                                                    aTTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGa                     <  2:3012509/93‑1 (MQ=255)
                                                                     ttACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTgga                    >  2:2405937/1‑91 (MQ=255)
                                                                       acacGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAAc                  <  1:1356331/93‑1 (MQ=255)
                                                                         acGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCa                <  2:3240414/93‑1 (MQ=255)
                                                                         acGGGGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAAGCa                >  1:182026/1‑93 (MQ=255)
                                                                          cGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAg               <  2:11470/93‑1 (MQ=255)
                                                                            gtcaaTCGCCAGGTAGTCGACGGTTAACGATTCCTTGTATATCTGACCCCGATTTATGTATGCAACTGGATGCCTTGAATGCTGAAACCAGTa             <  2:843544/90‑1 (MQ=255)
                                                                              gAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATc           <  2:4436785/93‑1 (MQ=255)
                                                                               aaTCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATcc          <  2:4298137/93‑1 (MQ=255)
                                                                                 tCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccct        <  2:437547/93‑1 (MQ=255)
                                                                                 tCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccct        <  2:1536519/93‑1 (MQ=255)
                                                                                 tCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccct        >  1:1267539/1‑93 (MQ=255)
                                                                                 tCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccct        >  2:2352943/1‑93 (MQ=255)
                                                                                  cGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctg       >  1:727044/1‑93 (MQ=255)
                                                                                    ccAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctgcc     <  2:1669050/93‑1 (MQ=255)
                                                                                     cAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctgccc    >  1:3507434/1‑93 (MQ=255)
                                                                                      aGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctgccct   >  1:3854373/1‑93 (MQ=255)
                                                                                       ggTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctgccctg  >  2:2956267/1‑93 (MQ=255)
                                                                                       ggTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATccctgccctg  >  1:2944157/1‑93 (MQ=255)
                                                                                          |                                                                                         
AGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTG  >  NC_000913/1919783‑1919962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CAGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCTAA  >  NC_000913/1919782‑1919966
                                                                                           |                                                                                             
CAGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAAT                                                                                             >  SRR4302535.249897/1‑94 (MQ=60)
CAGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAAT                                                                                             <  SRR4302535.4467363/94‑1 (MQ=60)
 AGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATC                                                                                            <  SRR4302535.179124/94‑1 (MQ=60)
  GCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCG                                                                                           >  SRR4302535.1787909/1‑94 (MQ=60)
   CTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGGAATCGA                                                                                          >  SRR4302535.2471545/1‑94 (MQ=60)
     AAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAAC                                                                                        <  SRR4302535.3405054/94‑1 (MQ=60)
      AATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACTGTGAATCGCCAGGTAATCGAACG                                                                                       <  SRR4302535.4283945/94‑1 (MQ=60)
        TGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGTT                                                                                     <  SRR4302535.3010220/94‑1 (MQ=60)
         GGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATTGCGAGGTAATCGAACGgga                                                                                    >  SRR4302535.2089764/1‑91 (MQ=60)
          GAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAA                                                                                   >  SRR4302535.38353/1‑94 (MQ=60)
           AGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAAC                                                                                  >  SRR4302535.1767923/1‑94 (MQ=60)
            GAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACC                                                                                 <  SRR4302535.1300334/94‑1 (MQ=60)
             AGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCA                                                                                >  SRR4302535.1550527/1‑94 (MQ=60)
                 CGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCC                                                                            <  SRR4302535.4715847/94‑1 (MQ=60)
                 CGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCCCCAGGTAATCGAACGTTAACCATTCC                                                                            <  SRR4302535.2635348/94‑1 (MQ=60)
                  GAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCT                                                                           >  SRR4302535.2354396/1‑94 (MQ=60)
                    AGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAGTCGCCAGGTAATCGAACGTTAACCATTCGTTG                                                                         >  SRR4302535.1720057/1‑94 (MQ=60)
                    AGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTG                                                                         <  SRR4302535.620427/94‑1 (MQ=60)
                       TGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAA                                                                      <  SRR4302535.3391328/94‑1 (MQ=60)
                           AACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCT                                                                  <  SRR4302535.4541204/94‑1 (MQ=60)
                           AACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCT                                                                  >  SRR4302535.582684/1‑94 (MQ=60)
                           AACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCT                                                                  <  SRR4302535.2227161/94‑1 (MQ=60)
                           AACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCT                                                                  <  SRR4302535.994589/94‑1 (MQ=60)
                            ACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTG                                                                 >  SRR4302535.3098324/1‑94 (MQ=60)
                              CAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGAC                                                               >  SRR4302535.1984285/1‑94 (MQ=60)
                               AGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACC                                                              >  SRR4302535.4414889/1‑94 (MQ=60)
                               AGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACC                                                              <  SRR4302535.3224918/94‑1 (MQ=60)
                                     CGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATT                                                        <  SRR4302535.4252158/94‑1 (MQ=60)
                                     CGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATT                                                        <  SRR4302535.3427569/94‑1 (MQ=60)
                                     CGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATT                                                        >  SRR4302535.4286076/1‑94 (MQ=60)
                                        ATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTAT                                                     <  SRR4302535.3218408/94‑1 (MQ=60)
                                          AGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGT                                                   >  SRR4302535.2961955/1‑94 (MQ=60)
                                           GGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTA                                                  >  SRR4302535.3594168/1‑94 (MQ=60)
                                           GGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTA                                                  <  SRR4302535.2609140/94‑1 (MQ=60)
                                            GCGCTTTTGAAATCGACGACGGCGAACTACACGGTGAATCGCTAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTAT                                                 <  SRR4302535.2094612/94‑1 (MQ=60)
                                             CGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATG                                                <  SRR4302535.3461200/94‑1 (MQ=60)
                                               CTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCA                                              >  SRR4302535.736373/1‑94 (MQ=60)
                                               CTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCA                                              >  SRR4302535.571593/1‑94 (MQ=60)
                                                 TTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAAC                                            <  SRR4302535.774878/94‑1 (MQ=60)
                                                  TTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACT                                           <  SRR4302535.4479075/94‑1 (MQ=60)
                                                   TGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTG                                          >  SRR4302535.2529183/1‑94 (MQ=60)
                                                    GAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGG                                         <  SRR4302535.4287620/94‑1 (MQ=60)
                                                      AATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGAT                                       <  SRR4302535.1197341/94‑1 (MQ=60)
                                                      AATCGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGAT                                       <  SRR4302535.1791819/94‑1 (MQ=60)
                                                         CGACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCC                                    >  SRR4302535.2880361/1‑94 (MQ=60)
                                                          GACGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCT                                   <  SRR4302535.4368722/94‑1 (MQ=60)
                                                            CGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGG                                 <  SRR4302535.4458038/94‑1 (MQ=60)
                                                            CGACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGG                                 <  SRR4302535.4154895/94‑1 (MQ=60)
                                                             GACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGG                                >  SRR4302535.5805/1‑94 (MQ=60)
                                                             GACGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGG                                <  SRR4302535.4455342/94‑1 (MQ=60)
                                                               CGGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGAT                              <  SRR4302535.221155/94‑1 (MQ=60)
                                                                GGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATG                             <  SRR4302535.1123300/94‑1 (MQ=60)
                                                                GGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATG                             >  SRR4302535.2342112/1‑94 (MQ=60)
                                                                GGCGAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATG                             <  SRR4302535.1765638/94‑1 (MQ=60)
                                                                   GAATTACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTG                          >  SRR4302535.1205806/1‑94 (MQ=60)
                                                                       TACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAAC                      >  SRR4302535.4715497/1‑94 (MQ=60)
                                                                        ACACGGTGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACC                     <  SRR4302535.1366036/94‑1 (MQ=60)
                                                                         CACGGGGAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAAGCA                    >  SRR4302535.183286/1‑94 (MQ=60)
                                                                               GAATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCC              <  SRR4302535.946432/94‑1 (MQ=60)
                                                                                AATCGCCAGGTAAGCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCC             <  SRR4302535.1796905/94‑1 (MQ=60)
                                                                                 ATCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCT            >  SRR4302535.1276608/1‑94 (MQ=60)
                                                                                  TCGCCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTG           >  SRR4302535.732151/1‑94 (MQ=60)
                                                                                     CCAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCC        >  SRR4302535.3531810/1‑94 (MQ=60)
                                                                                      CAGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCT       >  SRR4302535.3880914/1‑94 (MQ=60)
                                                                                       AGGTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTG      >  SRR4302535.2964853/1‑94 (MQ=60)
                                                                                         GTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCT    <  SRR4302535.1050674/94‑1 (MQ=60)
                                                                                         GTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCT    <  SRR4302535.1514200/94‑1 (MQ=60)
                                                                                         GTAATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCT    >  SRR4302535.2897456/1‑94 (MQ=60)
                                                                                           AATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCTAA  <  SRR4302535.3579577/94‑1 (MQ=60)
                                                                                           AATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCTAA  >  SRR4302535.2246727/1‑94 (MQ=60)
                                                                                           |                                                                                             
CAGCTAAATGGAGAGCACGAAGATGAAAACCAGTGTGCGCATAGGCGCTTTTGAAATCGACGACGGCGAATTACACGGTGAATCGCCAGGTGATCGAACGTTAACCATTCCTTGTAAATCTGACCCCGATTTATGTATGCAACTGGATGCCTGGGATGCTGAAACCAGTATCCCTGCCCTGCTAA  >  NC_000913/1919782‑1919966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑